I will leave the player and the ground as-is, though I will reset the player back to its starting position. Only resetting does not seem to work. Fruit seems to hang around and, if I check scene.children, it does not seem to correspond to what is actually in the scene:

There should at least be 5 objects in the scene: the camera, the ground, the player, and two fruit. But the scene is only reporting three. Strange.

In the end, I can come up with no other way to do this than to reach under the Physijs covers:

for (var i in scene._objects) {
if (scene._objects[i].is_fruit) {
scene.remove(scene._objects[i]);
}
}